Why is my overall delta percentage of 0.9% (bottom right) less than all 5 of the values that make it up (1.7%, 3.2%, ...)? I know with the difference in magnitude of each row and column that it could skew the percentages, and I know that I'm subtracting percentages, but I'd still expect at least 1 of the values in the right-most column to be lower than 0.9%!

Your "Totals" row is not a fair average of the other rows at all; when you just look at the percentages, you lose all information about which rows have big numbers and which rows have small numbers. In your example, the upper rows for A and B are comparatively more significant, which skews the total B/A percentage up, while the lower rows for C and D are comparatively more significant, skewing the total D/C percentage down.

If you really want to measure some kind of average of the difference of the percentages among all five rows, you have several options-- you could just take the average of your rightmost column, or you could take a weighted average (weighted by A or C, maybe). The best choice depends on what the data means and on precisely what you want to measure.